Genome-Wide Analysis of the Fusarium oxysporum mimp Family of MITEs and Mobilization of Both Native and De Novo Created mimps

Abstract

We have performed a genome-wide analysis of the mimp family of miniature inverted-repeat transposable elements, taking advantage of the recent release of the F. oxysporum genome sequence. Using different approaches, we detected 103 mimp elements, corresponding to 75 nonredundant copies, half of which are located on a single small chromosome. Phylogenetic analysis identified at least six subfamilies, all remarkably homogeneous in size and sequence. Based on high sequence identity in the terminal inverted repeats (TIRs), mimp elements were connected to different impala members. To gain insights into the mechanisms at the origin and amplification of mimps, we studied the potential of impala to cross-mobilize different mimps, native but also created de novo by inserting a short DNA segment between two TIRs. Our results show that TIR sequences are the main requirement for mobilization but that additional parameters in the internal region are likely to influence transposition efficiency. Finally, we show that integration site preference of native versus newly transposed mimps greatly varies in the host genomes used in this study.

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

“…Mimps are uniformly small in size, ranging from 200 – 220 bp. Their central region has no coding capacity and is flanked by ~27 bp TIRs that resemble the TIRs of the Tc1/mariner transposase Impala [51]. Impalas have been shown to transpose mimps in a heterologous system [52].…”

“…However, none of the Impala copies in the Fol genome are intact, suggesting that mimps are not currently transposed in Fol4287 . In the past there appear to have been several bursts of mimp amplification resulting in at least six mimp subfamilies present in Fol [51]. Strikingly, more than half of the mimps in Fol4287 are present on the pathogenicity chromosome and the other mimps, with four exceptions, are restricted to the LS regions (Table 3) [51].…”

Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors

“…MITEs are short (, 500 bp) genetic elements, structurally similar to defective class II genetic elements (Bergemann et al 2008). Two novel families of MITEs, Vege and Mar from Drosophila willistoni, belong to the hAT superfamily of transposable elements (Holyoake and Kidwell 2003).…”

Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses

“…In plants thus far examined, MITEs have an integration site bias for genic regions of the genome (e.g., Bureau and Wessler 1994a, 1994b; Mao et al 2000) and thus likely influence expression of associated genes. MITEs in fungi have received little attention, with just two families being characterized: Guest in Neurospora crassa (Yeadon and Catcheside 1995; Ramussen et al 2004) and mimp in Fusarium oxysporum (Hua-Van et al 2000; Dufresne et al 2007; Bergemann et al 2008). However, recently, a number of uncharacterized MITEs have been reported in fungal genome sequences (Martin et al 2008; Spanu et al 2010).…”